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Supplementary scientific material presenting figures and datasets on genetic structure, epigenetic variation, methylation patterns, primer sequences, environmental parameters, and population differentiation of Corydalis yanhusuo across cultivated and natural populations.
Document type: Supplementary material to a scientific research article
Subject: Genetic and epigenetic variation in Corydalis yanhusuo populations
Species: Corydalis yanhusuo
Analytical methods: STRUCTURE analysis; dbRDA; AFLP; MSAP
Content: Supplementary figures (S1–S2) and tables (S1–S6)
Populations analyzed: 17 populations (cultivated and natural)
Data included: Methylation frequencies; primer and adapter sequences; monthly mean weather parameters; pairwise FST values
Genetic markers: AFLP
Epigenetic markers: MSAP
Chemical variables: Tetrahydropalmatine; Protopine; Palmatine; Berberine
Environmental variables: Air pressure; temperature; relative humidity; precipitation; sunshine duration
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Supplemental Figure Legends: Transcriptional and Epigenetic Analyses of CDX2 and HNF4A in Human and Mouse Gastrointestinal Tissues
Document Type: Supplemental figure legends
Field: Molecular biology
Research Area: Gastrointestinal epithelium and intestinal metaplasia
Subjects: CDX2, HNF4A, SOX2, gastric organoids, Barrett’s esophagus, gastric intestinal metaplasia
Biological Material: Human gastrointestinal tissues and mouse stomach organoids
Methods: Single-cell RNA-seq, bulk RNA-seq, ATAC-seq, CUT&RUN, ChIP-seq, GSEA, enhancer analysis, immunohistochemistry, qRT-PCR
Referenced Studies: Busslinger et al. 2021b; Nowicki-Osuch et al. 2021; Owen et al. 2018; Companioni et al. 2017; Singh et al. 2021; Gao and Kaestner 2010; Wang et al. 2013
Key Topics: Transcriptional profiling, chromatin accessibility, enhancer activity, transcription factor binding, intestinalization of gastric epithelium
Species: Homo sapiens; Mus musculus
Pathological Context: Barrett’s esophagus; gastric intestinal metaplasia
The exploitation and use of epigenetic factors in cancer therapy
Year: 2023
Author: Jacob Ivy
Field of study: Biology, Pre-Med
Department: Microbiology and Molecular Genetics, Oklahoma State University
Location: Stillwater, OK, USA
Type of document: Research article
Keywords: Epigenetics, Biomarkers, Nanoparticles, Methylation
Target audience: Researchers and students in molecular biology and oncology
Scope: Diagnostic and therapeutic applications of epigenetic factors in cancer
Recent developments: Site-specific cancer drugs, epigenetic biomarkers, nanoparticle delivery systems
Sources cited: Roberti et al., 2019; Villanueva et al., 2020
Association analysis between an epigenetic alcohol risk score and blood pressure in the Agricultural Lung Health Study and KORA cohorts
Year: 2006-2014
Region: Iowa and North Carolina, USA; Augsburg, Germany
Topic: Epigenetics, Alcohol consumption, Blood pressure
Document type: Supplemental materials / Research data description
Institution: National Institute of Environmental Health Sciences; Cooperative Health Research in the Region Augsburg (KORA)
Authors: Bui, Keshawarz, Wang et al.
Study design: Case-control study (ALHS); Population-based cohort (KORA)
Participants: Farmers and spouses (ALHS); General population aged 25-74 (KORA)
Sample size: 3,301 (ALHS); 1,802 (KORA F4)
Data collected: DNA methylation, clinical and behavioral phenotypes, alcohol consumption, smoking status
Consent and approval: Informed consent obtained; Institutional Review Board approval (ALHS)
Funding: Intramural Research Program of the NIH, National Cancer Institute, American Recovery and Reinvestment Act funds
Analytical methods: DNA methylation measurement with EPIC and 450K BeadChips, quality control, normalization, cell type estimation, statistical regression analyses
SINGLE-CELL TRANSCRIPTOME AND EPIGENETIC PROFILING OF THE PITUITARY GLAND IN NILE TILAPIA
Year: 2024
Region / City: Bodø, Norway; Edinburgh, Scotland; Barcelona, Spain
Subject: Reproductive endocrinology, teleost puberty
Document type: Research article
Institution: Nord University, The Roslin Institute, Institute of Marine Science (ICM)
Authors: L. Colonna, I. Konstantinidis, R.R. Daniels, D. Robledo, J.M.O. Fernandes
Target audience: Researchers in marine biology and fish physiology
Methodology: Single-cell RNA-seq and ATAC-seq profiling
Model organism: Nile tilapia (Oreochromis niloticus)
Experimental conditions: Continuous and ambient light exposure for 4 months
Purpose: Identification of pituitary cell types and markers associated with puberty onset in teleosts
Reference: M. Li, L. Sun, L. Zhou & D. Wang (2024). Gen Comp Endocrinol 345:114395
Research Strategy for EpiNet: Incorporating Epigenetic Regulators into Gene Regulatory Network Inference
Document type: Research proposal section
Research area: Systems biology and epigenetics
Scientific field: Gene regulatory network modeling
Research focus: Integration of epigenetic regulators into gene network inference
Model organism: Arabidopsis thaliana
Key regulator studied: SET Domain Group 8 (SDG8)
Homologous human protein: SETD2
Epigenetic mechanism: H3K36 histone methylation
Biological processes referenced: Gene regulation and chromatin modification
Methodological approaches: Time-course transcriptome analysis, predictive network modeling, dynamic Bayesian networks, state-space modeling
Data sources referenced: Epigenomics datasets and ENCODE resources
Research objectives: Identification of genomic targets of epigenetic regulators and evaluation of their role as predictors in gene regulatory network models
Proposed framework: EpiNet
Research components: Significance, Innovation, and Approaches
Experimental strategy: Integration of experimental perturbation data with computational network inference
Topics: Corydalis yanhusuo Epigenetic